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Workflow and Tool Execution

The execute command provides tools to execute CWL documents locally or on a remote server (soonish™).

Usage

Execution of CWL Files locally or on remote servers

Usage: s4n execute <COMMAND>

Commands:
  local  Runs CWL files locally using a custom runner or cwltool [aliases: l]      
  make-template  Creates job file template for execution (e.g. inputs.yaml)
  help   Print this message or the help of the given subcommand(s)

Options:
  -h, --help  Print help

execute local

There are two options for local execution. Using the CWL reference runner cwltool which needs to be installed as extern dependency using pip install cwltool or the SciWIn client runner which supports a large subset of CWL but lacks support containerization. You may ask yourself: why is there a custom runner? Because cwltool only supports Windows using the Windows Subsystem for Linux (wsl) which is deactivated on many enterprise systems. The intention is to have a simple tool to test the generated CWL documents before sending them to the remote server. The usage of the internal runner, which is the default one, is similar to the usage of cwltool. It accepts the cwl file as first parameter and the inputs following at the end of the commands either as command line string or yaml file.

Usage

Runs CWL files locally using a custom runner or cwltool

Usage: s4n execute local [OPTIONS] <FILE> [ARGS]...

Arguments:
  <FILE>     CWL File to execute
  [ARGS]...  Other arguments provided to cwl file

Options:
  -r, --runner <RUNNER>   Choose your cwl runner implementation [default: custom] [possible values: cwltool, custom]
      --outdir <OUT_DIR>  A path to output resulting files to
      --quiet             Runner does not print to stdout
  -h, --help              Print help

execute remote

Not yet implemented

execute make-template

s4n execute make-template is able to create a dummy CWL job file (e.g. inputs.yaml) that can be used as a template for an upoming execution of CWL.

Usage

Creates job file template for execution (e.g. inputs.yaml)

Usage: s4n execute make-template <CWL>

Arguments:
  <CWL>  CWL File to create input template for

Options:
  -h, --help  Print help